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Yorodumi- PDB-6txs: The structure of the FERM domain and helical linker of human moes... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6txs | |||||||||
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Title | The structure of the FERM domain and helical linker of human moesin bound to a CD44 peptide | |||||||||
Components |
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Keywords | PROTEIN BINDING / PIP / FERM domain / Alzheimer's disease / CD44 | |||||||||
Function / homology | Function and homology information positive regulation of monocyte aggregation / regulation of lymphocyte migration / T cell aggregation / regulation of organelle assembly / Hyaluronan uptake and degradation / T cell migration / positive regulation of early endosome to late endosome transport / membrane to membrane docking / hyaluronic acid binding / monocyte aggregation ...positive regulation of monocyte aggregation / regulation of lymphocyte migration / T cell aggregation / regulation of organelle assembly / Hyaluronan uptake and degradation / T cell migration / positive regulation of early endosome to late endosome transport / membrane to membrane docking / hyaluronic acid binding / monocyte aggregation / macrophage migration inhibitory factor receptor complex / uropod / regulation of lamellipodium morphogenesis / immunological synapse formation / gland morphogenesis / hyaluronan catabolic process / positive regulation of protein localization to early endosome / cellular response to testosterone stimulus / establishment of epithelial cell apical/basal polarity / establishment of endothelial barrier / cellular response to fibroblast growth factor stimulus / positive regulation of heterotypic cell-cell adhesion / Sensory processing of sound by outer hair cells of the cochlea / positive regulation of podosome assembly / cartilage development / Sensory processing of sound by inner hair cells of the cochlea / wound healing, spreading of cells / cytokine receptor activity / microvillus membrane / leukocyte cell-cell adhesion / regulation of cell size / leukocyte migration / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / pseudopodium / Recycling pathway of L1 / negative regulation of DNA damage response, signal transduction by p53 class mediator / microvillus / lamellipodium membrane / Integrin cell surface interactions / T cell proliferation / cell adhesion molecule binding / collagen binding / T cell activation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Degradation of the extracellular matrix / cell-matrix adhesion / secretory granule membrane / filopodium / cell projection / cell periphery / Cell surface interactions at the vascular wall / adherens junction / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / structural constituent of cytoskeleton / cell-cell adhesion / positive regulation of protein catabolic process / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / Interferon gamma signaling / double-stranded RNA binding / Signaling by ALK fusions and activated point mutants / cell migration / apical part of cell / positive regulation of peptidyl-serine phosphorylation / actin binding / regulation of cell shape / basolateral plasma membrane / vesicle / positive regulation of ERK1 and ERK2 cascade / cytoskeleton / blood microparticle / cell adhesion / inflammatory response / apical plasma membrane / focal adhesion / signaling receptor binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / cell surface / extracellular space / extracellular exosome / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Bradshaw, W.J. / Katis, V.L. / Kelly, J.J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. | |||||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Discovery of FERM domain protein-protein interaction inhibitors for MSN and CD44 as a potential therapeutic approach for Alzheimer's disease. Authors: Du, Y. / Bradshaw, W.J. / Leisner, T.M. / Annor-Gyamfi, J.K. / Qian, K. / Bashore, F.M. / Sikdar, A. / Nwogbo, F.O. / Ivanov, A.A. / Frye, S.V. / Gileadi, O. / Brennan, P.E. / Levey, A.I. / ...Authors: Du, Y. / Bradshaw, W.J. / Leisner, T.M. / Annor-Gyamfi, J.K. / Qian, K. / Bashore, F.M. / Sikdar, A. / Nwogbo, F.O. / Ivanov, A.A. / Frye, S.V. / Gileadi, O. / Brennan, P.E. / Levey, A.I. / Axtman, A.D. / Pearce, K.H. / Fu, H. / Katis, V.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6txs.cif.gz | 90.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6txs.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6txs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6txs_validation.pdf.gz | 434.8 KB | Display | wwPDB validaton report |
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Full document | 6txs_full_validation.pdf.gz | 435.9 KB | Display | |
Data in XML | 6txs_validation.xml.gz | 14 KB | Display | |
Data in CIF | 6txs_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/6txs ftp://data.pdbj.org/pub/pdb/validation_reports/tx/6txs | HTTPS FTP |
-Related structure data
Related structure data | 6txqC 8cirC 8cisC 8citC 8ciuC 1e5wS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41141.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MSN / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P26038 |
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#2: Protein/peptide | Mass: 973.233 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Octapeptide based on the intracellular C-terminal tail of CD44 Source: (synth.) Homo sapiens (human) / References: UniProt: P16070 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.42 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M potassium thiocyanate, 0.1M bis-tris pH 7.0, 10% ethylene glycol, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→84.83 Å / Num. obs: 23382 / % possible obs: 99.7 % / Redundancy: 23.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.048 / Rrim(I) all: 0.173 / Χ2: 0.9 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 11.7 % / Rmerge(I) obs: 3.189 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1977 / CC1/2: 0.46 / Rpim(I) all: 1.372 / Rrim(I) all: 3.492 / Χ2: 0.82 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1E5W Resolution: 2.2→84.83 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.263 / WRfactor Rwork: 0.215 / SU B: 11.746 / SU ML: 0.264 / Average fsc free: 0.7371 / Average fsc work: 0.7584 / Cross valid method: FREE R-VALUE / ESU R: 0.275 / ESU R Free: 0.225 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.379 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→84.83 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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